scholarly journals Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Ning Yan ◽  
Ting Yang ◽  
Xiu-Ting Yu ◽  
Lian-Guang Shang ◽  
De-Ping Guo ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Wild Rice ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Divergence Time ◽  
Close Relation ◽  
Abscission Layer ◽  
Zizania Latifolia ◽  
Seed Shattering ◽  
Chromosome Level

AbstractChinese wild rice (Zizania latifolia; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 38,852 genes, with 52.89% of the genome comprising repetitive sequences. Phylogenetic analyses revealed close relation of Z. latifolia to Leersia perrieri and Oryza species, with a divergence time of 19.7–31.0 million years. Collinearity and transcriptome analyses revealed candidate genes related to seed shattering, providing basic information on abscission layer formation and degradation in Z. latifolia. Moreover, two genomic blocks in the Z. latifolia genome showed good synteny with the rice phytocassane biosynthetic gene cluster. The updated genome will support future studies on the genetic improvement of Chinese wild rice and comparative analyses between Z. latifolia and other plants.

scholarly journals Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

2021 ◽  
Vol 12 ◽  
Author(s):  
Jielong Zhou ◽  
Peifu Wu ◽  
Zhongping Xiong ◽  
Naiyong Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Thaumetopoea Pityocampa ◽  
High Quality ◽  
Protein Coding ◽  
Peptidoglycan Recognition Protein ◽  
Recognition Protein ◽  
Chromosome Level

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

scholarly journals Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Boping Tang ◽  
Daizhen Zhang ◽  
Haorong Li ◽  
Senhao Jiang ◽  
Huabin Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Repetitive Sequences ◽  
Asia Pacific ◽  
Portunus Trituberculatus ◽  
Swimming Crab ◽  
Protein Coding ◽  
Eukaryotic Genes ◽  
Long Reads ◽  
Commercial Species ◽  
Chromosome Level

Abstract Background The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking. Findings Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology. Conclusions We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.

scholarly journals Effect of quantitative trait loci for seed shattering on abscission layer formation in Asian wild rice Oryza rufipogon

2014 ◽  
Vol 64 (3) ◽  
pp. 199-205 ◽  
Author(s):  
Than Myint Htun ◽  
Chizuru Inoue ◽  
Orn Chhourn ◽  
Takashige Ishii ◽  
Ryo Ishikawa
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Layer Formation ◽  
Abscission Layer ◽  
Seed Shattering ◽  
Trait Loci

scholarly journals A stepwise route to domesticate rice by controlling seed shattering and panicle shape

2021 ◽  
Author(s):  
Ryo Ishikawa ◽  
Cristina Cobo Castillo ◽  
Than Myint Htun ◽  
Koji Numaguchi ◽  
Kazuya Inoue ◽  
...  
Keyword(s):  
Wild Rice ◽  
Genetic Change ◽  
Abscission Layer ◽  
Single Nucleotide ◽  
Seed Shattering ◽  
Asian Rice ◽  
Rice Genetic ◽  
Initial Selection ◽  
Rice Domestication ◽  
Selection Of

AbstractRice (Oryza sativa L.) is consumed by more than half of the world’s population, but despite its global importance the mechanisms of domestication remain unclear. During domestication, wild rice (O. rufipogon Griff.) was transformed by acquiring non-seed-shattering behaviour, an important genetic change that allowed humans to increase grain yield. However, we show previously identified loci, sh4 and qSH3, are individually insufficient to explain loss of seed shattering nor increases in harvest yield in wild rice. We identify the complementary interaction of key mutations for abscission layer interruption and panicle architecture that were causal in the early domestication of Asian rice. An interruption of abscission layer formation requires both sh4 and qSH3, which presents an apparent barrier to selection of shattering loss. We identified the causal single nucleotide polymorphism at qSH3 within a seed-shattering gene OsSh1 conserved in indica and japonica subspecies, but absent in the circum-aus group of rice. We demonstrate through harvest experiments that seed-shattering alone does not significantly impact yield. Instead, we observed yield increases under a SRR3-controlled closed panicle formation, which is augmented by the integration of sh4 and qSH3 alleles causing a slight inhibition of abscission layer. Complementary manipulation of seed shattering and panicle shape result in a panicle structure that is mechanically stable. We propose a stepwise route in the earliest phase of rice domestication in which selection for visible SRR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3 and leading to loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 is insufficient on its own to cause abscission layer disruption and other genes, such as qSH3 are required, making mechanisms for the initial selection of non-shattering unclear. We show that shattering loss in wild rice genetic backgrounds does not increase yields. We identify an interaction in which a second trait, closed panicle formation controlled by SPR3, both increases yield and facilitates recruitment of sh4 and qSH3 which synergistically augment yield, leading to a stepwise route for rice domestication.

scholarly journals Chromosome Genome Assembly of Cromileptes altivelis Reveals Loss of Genome Fragment in Cromileptes Compared with Epinephelus Species

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1873
Author(s):  
Yang Yang ◽  
Lina Wu ◽  
Zhuoying Weng ◽  
Xi Wu ◽  
Xi Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Growth Traits ◽  
Divergence Time ◽  
Single Copy ◽  
Future Research ◽  
High Quality ◽  
Protein Coding ◽  
Substance Metabolism ◽  
Mapk Signal Pathway ◽  
Chromosome Level

The humpback grouper (Cromileptes altivelis), an Epinephelidae species, is patchily distributed in the reef habitats of Western Pacific water. This grouper possesses a remarkably different body shape and notably low growth rate compared with closely related grouper species. For promoting further research of the grouper, in the present study, a high-quality chromosome-level genome of humpback grouper was assembled using PacBio sequencing and high-throughput chromatin conformation capture (Hi-C) technology. The assembled genome was 1.013 Gb in size with 283 contigs, of which, a total of 143 contigs with 1.011 Gb in size were correctly anchored into 24 chromosomes. Moreover, a total of 26,037 protein-coding genes were predicted, of them, 25,243 (96.95%) genes could be functionally annotated. The high-quality chromosome-level genome assembly will provide pivotal genomic information for future research of the speciation, evolution and molecular-assisted breeding in humpback groupers. In addition, phylogenetic analysis based on shared single-copy orthologues of the grouper species showed that the humpback grouper is included in the Epinephelus genus and clustered with the giant grouper in one clade with a divergence time of 9.86 Myr. In addition, based on the results of collinearity analysis, a gap in chromosome 6 of the humpback grouper was detected; the missed genes were mainly associated with immunity, substance metabolism and the MAPK signal pathway. The loss of the parts of genes involved in these biological processes might affect the disease resistance, stress tolerance and growth traits in humpback groupers. The present research will provide new insight into the evolution and origin of the humpback grouper.

scholarly journals Genome Assembly of Salicaceae Populus deltoides (Eastern Cottonwood) I-69 Based on Nanopore Sequencing and Hi-C Technologies

2021 ◽  
Author(s):  
Shengjun Bai ◽  
Hainan Wu ◽  
Jinpeng Zhang ◽  
Zhiliang Pan ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Populus Deltoides ◽  
Wood Quality ◽  
Repetitive Sequences ◽  
Nanopore Sequencing ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Eastern Cottonwood ◽  
Genomic Resource ◽  
Chromosome Level

Abstract Populus deltoides has important ecological and economic values, widely used in poplar breeding programs due to its superior characteristics such as rapid growth and resistance to disease. Although the genome sequence of P. deltoides WV94 is available, the assembly is fragmented. Here, we reported an improved chromosome-level assembly of the P. deltoides cultivar I-69 by combining Nanopore sequencing and chromosome conformation capture (Hi-C) technologies. The assembly was 429.3 Mb in size and contained 657 contigs with a contig N50 length of 2.62 Mb. Hi-C scaffolding of the contigs generated 19 chromosome-level sequences, which covered 97.4% (418 Mb) of the total assembly size. Moreover, repetitive sequences annotation showed that 39.28% of the P. deltoides genome was composed of interspersed elements, including retroelements (23.66%), DNA transposons (6.83%), and unclassified elements (8.79%). We also identified a total of 44 362 protein-coding genes in the current P. deltoides assembly. Compared with the previous genome assembly of P. deltoides WV94, the current assembly had some significantly improved qualities: the contig N50 increased 3.5-fold and the proportion of gaps decreased from 3.2% to 0.08%. This high-quality, well-annotated genome assembly provides a reliable genomic resource for identifying genome variants among individuals, mining candidate genes that control growth and wood quality traits, and facilitating further application of genomics-assisted breeding in populations related to P. deltoides.

scholarly journals Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

2021 ◽  
Author(s):  
Kenta Shirasawa ◽  
Sogo Nishio ◽  
Shingo Terakami ◽  
Roberto Botta ◽  
Daniela Torello Marinoni ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Sequence Data ◽  
Repetitive Sequences ◽  
Genome Structure ◽  
Resistance Mechanisms ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Castanea Crenata ◽  
Long Read ◽  
Chromosome Level

Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids.

scholarly journals A high-quality chromosome-level genome of wild Rosa rugosa

DNA Research ◽  
2021 ◽  
Vol 28 (5) ◽  
Author(s):  
Fengqi Zang ◽  
Yan Ma ◽  
Xiaolong Tu ◽  
Ping Huang ◽  
Qichao Wu ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Duplication Event ◽  
Genome Sequences ◽  
Rosa Rugosa ◽  
High Quality ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Chromosome Level

Abstract Rosa rugosa is an important shrub with economic, ecological, and pharmaceutical value. A high-quality chromosome-scale genome for R. rugosa sequences was assembled using PacBio and Hi-C technologies. The final assembly genome sequences size was about 407.1 Mb, the contig N50 size was 2.85 Mb, and the scaffold N50 size was 56.6 Mb. More than 98% of the assembled genome sequences were anchored to seven pseudochromosomes (402.9 Mb). The genome contained 37,512 protein-coding genes, with 37,016 genes (98.68%) that were functionally annotated, and 206.67 Mb (50.76%) of the assembled sequences are repetitive sequences. Phylogenetic analyses indicated that R. rugosa diverged from Rosa chinensis ∼6.6 million years ago, and no lineage-specific whole-genome duplication event occurred after divergence from R. chinensis. Chromosome synteny analysis demonstrated highly conserved synteny between R. rugosa and R. chinensis, between R. rugosa and Prunus persica as well. Comparative genome and transcriptome analysis revealed genes related to colour, scent, and environment adaptation. The chromosome-level reference genome provides important genomic resources for molecular-assisted breeding and horticultural comparative genomics research.

A Chromosome-Level Genome Assembly Identifies the Origin of Neo-Y Chromosome to the Unique X 1X 2Y System

2019 ◽  
Author(s):  
Yongshuang Xiao ◽  
Zhizhong Xiao ◽  
Daoyuan Ma ◽  
Chenxi Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Genome Assembly ◽  
Chromosome Level
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